Clostridium innocuum (DSM 100998, BSM-380-WT-2D)

Name: Clostridium innocuum (DSM 100998, BSM-380-WT-2D)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158912

Type strain

Strain Designation BSM-380-WT-2D

Culture col. no. DSM 100998 BSM-380-WT-2D

NCBI tax ID(s) 1522

Special Collections DSMZ Pig DZIF

History DSMZ <- D. Wylensek, TU Munich, Freising-Weihenstephan, Germany; BSM-380-WT-2D

Links

Clostridium innocuum BSM-380-WT-2D is a bacterium that was isolated from feces; pig, 8 weeks old, wild type.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407201

DSM 100998

@ref 20215

Last LPSN update 2026-05-29 08:44:04

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium innocuum

Full scientific name Clostridium innocuum Smith and King 1962 (Approved Lists 1980)

BacDive ID	Other strains from **Clostridium innocuum** (10)	Type strain
2603	C. innocuum B-3, DSM 1286, ATCC 14501, NCIB 10674, JCM ... (type strain)
130922	C. innocuum I46, DSM 26113
130921	C. innocuum A-C3-1, DSM 29132
2604	C. innocuum SB23, DSM 22910
149069	C. innocuum CCUG 36812
151996	C. innocuum CCUG 45485
152489	C. innocuum CCUG 46922
155352	C. innocuum CCUG 57429
158913	C. innocuum H4_16, DSM 108163
160008	C. innocuum Cla-CZ-133, DSM 107457

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65734	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)		Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
65734	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	94.886

Spore formation

@ref	Spore formation	Confidence
125439		90.571

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68367	17057 ChEBI	cellobiose	+	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	+	builds acid from	from API 20A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	+	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	+	builds acid from	from API 20A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68367	gelatinase	-		from API 20A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
65734	-	-	+	+	-	-	-	+	-	-	-	+	-	+	+	-	-	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
65734	feces; pig, 8 weeks old, wild type	Kranzberg (Bavaria)	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
65734	2	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM969640v1 assembly for [Clostridium] innocuum BSM-380-WT-2D	contig	GCA_009696405	1522.112	8067392167	1522	65.74

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65734	[Clostridium] innocuum strain DSM 100998 16S ribosomal RNA gene, partial sequence	MN537452	1479		1522

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM969640v1 assembly for [Clostridium] innocuum BSM-380-WT-2D
NCBI: GCA_009696405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	94.89	no
125439	gram_stain	BacteriaNetⓘ	variable	73.77	no
125439	spore_formation	BacteriaNetⓘ	yes	90.57	no
125439	motility	BacteriaNetⓘ	yes	85.47	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] innocuum strain BSM-380-WT-2D
PATRIC: 1522.112

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	78.08	no
125438	anaerobic	anaerobicⓘ	yes	82.45	no
125438	spore-forming	spore-formingⓘ	no	54.96	no
125438	aerobic	aerobicⓘ	no	97.28	no
125438	thermophilic	thermophileⓘ	no	92.30	no
125438	flagellated	motile2+ⓘ	no	78.38	no

Literature

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#65734	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100998
#68367	Automatically annotated from API 20A .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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